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- PDB-3kgr: Crystal structure of the human leukocyte-associated Ig-like recep... -

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Basic information

Entry
Database: PDB / ID: 3kgr
TitleCrystal structure of the human leukocyte-associated Ig-like receptor-1 (LAIR-1)
ComponentsLeukocyte-associated immunoglobulin-like receptor 1
KeywordsIMMUNE SYSTEM / Ig-like domain / Cell membrane / Glycoprotein / Immune response / Immunoglobulin domain / Phosphoprotein / Receptor
Function / homology
Function and homology information


tertiary granule membrane / specific granule membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Neutrophil degranulation / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLYCINE / Leukocyte-associated immunoglobulin-like receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrondijk, T.H.C. / Huizinga, E.G. / Ballering, J.
CitationJournal: Blood / Year: 2010
Title: Crystal structure and collagen-binding site of immune inhibitory receptor LAIR-1: unexpected implications for collagen binding by platelet receptor GPVI
Authors: Brondijk, T.H.C. / de Ruiter, T. / Ballering, J. / Wienk, H. / Lebbink, R.J. / van Ingen, H. / Boelens, R. / Farndale, R.W. / Meyaard, L. / Huizinga, E.G.
History
DepositionOct 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukocyte-associated immunoglobulin-like receptor 1
B: Leukocyte-associated immunoglobulin-like receptor 1
C: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3785
Polymers35,2113
Non-polymers1672
Water7,981443
1
A: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)11,7371
Polymers11,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9043
Polymers11,7371
Non-polymers1672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)11,7371
Polymers11,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.395, 69.395, 54.258
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Leukocyte-associated immunoglobulin-like receptor 1 / LAIR-1 / hLAIR1


Mass: 11736.834 Da / Num. of mol.: 3 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAIR1 / Plasmid: pET3xa-hLAIR1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: Q6GTX8
#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.58 % / Mosaicity: 0.25 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 25-30% PEG-1500, 100mM succinic acid, 100mM sodium dihydrogen phosphate, 100mM glycine, 10mM CoCl2, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0396 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0396 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.294
ReflectionResolution: 1.8→60.098 Å / Num. obs: 26097 / % possible obs: 96.3 % / Observed criterion σ(I): -3.7 / Redundancy: 5.5 % / Biso Wilson estimate: 17.458 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 20.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.5 / Num. measured all: 12152 / Num. unique all: 3098 / Rsym value: 0.208 / % possible all: 78.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5

2gi7

2d3v

1ugn

2gw5


Resolution: 1.8→34.698 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.86 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 21.9 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.157 1319 5.06 %random
Rwork0.123 ---
all0.1242 ---
obs0.124 26079 96.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.86 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 99.03 Å2 / Biso mean: 23.233 Å2 / Biso min: 3.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.565 Å20 Å2-0 Å2
2--0.565 Å20 Å2
3----1.752 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 11 443 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092471
X-RAY DIFFRACTIONf_angle_d1.2793362
X-RAY DIFFRACTIONf_chiral_restr0.079356
X-RAY DIFFRACTIONf_plane_restr0.006454
X-RAY DIFFRACTIONf_dihedral_angle_d16.379934
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.8490.222760.18214761552
1.849-1.9030.265830.17816521735
1.903-1.9640.171830.15918781961
1.964-2.0350.182950.1519932088
2.035-2.1160.1691080.1419682076
2.116-2.2120.1581010.13519652066
2.212-2.3290.1631110.13819892100
2.329-2.4750.1681220.13719692091
2.475-2.6660.1531190.13419852104
2.666-2.9340.1511130.12219492062
2.934-3.3580.176910.1119802071
3.358-4.230.1121080.08319742082
4.23-34.7040.1541020.10619892091
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37540.48320.12750.66290.54890.2678-0.00020.01270.00120.09780.00410.13270.07850.0088-0.00260.05920.00410.00050.03110.00370.059827.55652.018642.0537
20.519-0.31480.14260.62880.73160.3388-0.0046-0.0412-0.0113-0.08550.01830.0110.0343-0.0322-0.0160.0837-0.0153-0.01360.03580.00680.052327.866328.020335.9665
30.81540.62060.13980.8661-0.09480.36760.032-0.1070.0304-0.0046-0.04460.1126-0.09810.10940.00910.0588-0.01670.00490.0877-0.01550.0547.99147.430419.5227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA25 - 123
2X-RAY DIFFRACTION2chain BB25 - 121
3X-RAY DIFFRACTION3chain CC25 - 123

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